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ABSTRACT: Long-read PacBio Sequencing of Chionographis japonica

PROVIDER: PRJEB58125 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10639451.fastq.gz	Fastqsanger.gz
	ERR10639452.fastq.gz	Fastqsanger.gz
	ERR10639453.fastq.gz	Fastqsanger.gz
	ERR10639454.fastq.gz	Fastqsanger.gz
	ERR10639455.fastq.gz	Fastqsanger.gz

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ChIP-seq of holocentric Chionographis japonica to determine the centromere distribution and genome organization

Project description:To determine the distribution of centromere units in the genome of holocentric Chionographis japonica, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. japonica and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chio satellite repeats (16%) in the C. japonica genome before immunoprecipitation. In addition, to determine the large-scale genome organization, we performed ChIPseq by targeting the evolutionarily conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2

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Project description:Here we describe CapTrap-Seq, an experimental workflow designed to address the problem of reduced transcript end detection by long-read RNA sequencing methods, especially at the 5' ends. We apply CapTrap-Seq to profile transcriptomes of the human heart and brain and we compared the obtained results with other library preparation approaches. CapTrap-Seq is a platform-agnostic method and here tested the method by using 3 different long-read sequencing platforms: MinION (ONT), Sequel (PacBaio) and Sequel II (PacBio).

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